Gut microbe annotation DB
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Entering edit mode
3.1 years ago
lotus28 ▴ 70

As a result of my study I have received a number of bacterial species that are important for developing a medical condition.

Now I would like to know, what are these bacteria's role in gut microbiome. I want to see which of them have invasive potential, what metabolites they feed on and what they produce, are they associated with any other conditions, if they are anaerobes or not, what antibiotics they are susceptible, how they react to dietary nutrients to etc.

Unfortunately, I have failed to find a data base that would contain all such features. I have considered Microbiome Directory, which is way too generic, ARDB, which is a rsistence DB, and MBGD, which is basically a gateway to KEGG. None of these provide a structured general outline of microbes.

Is there even such a data base? If it required paid access, I would gladly pay for it. It is a pity that there are dozens of DBs that cover all the aspects of macromolecules, but no analog of GO for microbiologists.

microbiome gut bacteria ecology microbiology • 662 views
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Entering edit mode
3.0 years ago

I am assuming you are using amplicon sequencing approach.

Currently, there is not tool or database which can tell you all information at once. Bu you can play around to gather such information.

  1. Use PICRUSt, to discover genes present in your data and their abundances (in terms of KO and COGs)
  2. Next you can do GO enrichment using these KOs
  3. For phenotypic information use BugBase

Unfortunately there is no tool for identifying antibiotic resistanct and pathogenic organisms from your dataset. If you are using 16S rRNA gene, it will not be wise to comment on antibiotic resistence and pathogenicity. (as getting species level identification is hard on basis of one gene) and these properties are strain specific also. (The resolution of 16S rRNA is not upto strain level)

Hope this will help you.

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